Approximately 8% of the genomes of mammals, including humans and mice, are comprised of retroviral elements acquired by infection of germ line cells during the course of evolution. Retroviral insertions in our genome number about 40,000 and are in the same range as the total number of genes encoded by our DNA. Many endogenous retrovirus elements are defective, however some appear to be intact, and several contain one or more viral genes that are expressed during development and certain physiological or pathological conditions. Little is known about the control of retrovirus expression or the influence of such expression on the physiology or pathology of the host. An extensively investigated group of endogenous retroviruses are those giving rise to polytropic murine leukemia viruses (MuLVs) in mice. In several instances polytropic MuLVs have been directly implicated in pathogenesis, including the induction of proliferative, immunological, and neurological disorders. Polytropic MuLVs are formed by recombination of exogenous ecotropic MuLVs with endogenous envelope sequences present in the genomes of inbred mouse strains and their generation results in a mixed retrovirus infection. We have investigated the interactions of retroviruses in mixed infections in vivo by co-inoculation of mice with polytropic and ecotropic MuLVs and observed remarkable alterations in the types and tempo of disease induced by different mixtures of viruses. These included a highly significant delay in the induction of proliferative disease with one polytropic MuLV and a profound synergistic effect resulting in the abrupt development of a neurological disease with another polytropic isolate. In both cases these effects were accompanied by extensive pseudotyping of the polytropic MuLV genome within ecotropic virions and a striking elevation of polytropic MuLV infection and replication in co-inoculated mice. Co-infection of in vitro cell cultures with ecotropic and polytropic MuLVs also results in extensive pseudotyping of the polytropic genome and a striking elevation in polytropic MuLV replication. Studies of the in vitro co-infected cells strongly suggest that the amplification of polytropic MuLV is the result of increased efficiency of incorporation of the polytropic genomic RNA into virions by the ecotropic packaging system. Another aspect of our studies involves the characterization of the family of endogenous retroviruses that participate in recombination to yield polytropic MuLVs. The participation of these endogenous retroviruses in recombination is not random and is different upon infection of mice with different exogenous viruses. We have characterized the endogenous retroviruses in NFS/N mice that could potentially give rise to the recombinant viruses and found that each could be distinguished by small nucleotide sequence differences. Comparison of the endogenous viruses to recombinant viruses derived after inoculation of an exogenous ecotropic MuLV indicated that only 3 of the approximately 25 to 30 endogenous retroviruses frequently participate in recombination. In additional studies we have found that mice infected with exogenous retroviruses release infectious virus particles containing RNA sequences characteristic of the transcriptional control elements of intact endogenous retroviruses. We are currently characterizing these viral genomes to determine if they correspond to previously undetected types of recombinant retroviruses or to intact endogenous retroviruses. The mobilization of intact endogenous retroviruses or the generation of recombinants containing endogenous transcriptional control elements is unprecedented and may have important implications for the involvement of endogenous retroviruses in disease processes. FY 2004 advance: All mammalian species contain a large number of retrovirus elements in their genomes that have accumulated by germ line infection over the course of evolution. The elements are expressed in a controlled manner during development and in certain pathological conditions and may play physiological or pathological roles in the host. We have characterized a group of endogenous retrovirus sequences in NFS/N mice that are known to be participants in the induction of proliferative diseases as well as other disorders. Their participation is mediated by recombination with exogenous retroviruses to generate new viruses, termed polytropic MuLVs that exhibit an altered host range of infection. It is known that the endogenous polytropic proviruses are not equally active in recombination and that recombination differs with different exogenous viruses. It was not known, however, precisely which of the endogenous elements participate in recombination. This has been elusive because of the very close similarity of the endogenous sequences to one another. Our earlier findings indicated that the viruses are distinguishable by minor sequence differences. These differences facilitated the precise identification of those proviruses that frequently participate in recombination. It was found that only 3 of approximately 25 to 30 of the endogenous viruses readily participate in recombination. Further, some exogenous viruses recombine with all three of the identified endogenous viruses whereas other exogenous viruses recombine with only two of the three sequences. These results, coupled with results of previous studies suggested a molecular mechanism for the specificity of recombination of the endogenous retroviruses with different exogenous viruses. Alamgir AS, Owens N, Lavignon M, Malik F, Evans LH. 2005. Precise Identification of Endogenous Proviruses of NFS/N Mice Participating in Recombination with Moloney Ecotropic Murine Leukemia Virus (MuLV) To Generate Polytropic MuLVs. J Virol:79,4664-71